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- PDB-3qce: Human receptor protein tyrosine phosphatase gamma, domain 1, in c... -

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Basic information

Entry
Database: PDB / ID: 3qce
TitleHuman receptor protein tyrosine phosphatase gamma, domain 1, in complex with 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid via soaking
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / negative regulation of epithelial cell migration / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / negative regulation of neuron projection development / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-NXY / Receptor-type tyrosine-protein phosphatase gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSheriff, S.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop
Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W.
#1: Journal: To be Published
Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms
Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S.
History
DepositionJan 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase gamma
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4388
Polymers71,4152
Non-polymers1,0236
Water2,954164
1
A: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1233
Polymers35,7081
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3155
Polymers35,7081
Non-polymers6074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.900, 82.500, 127.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 35707.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPG, PTPRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Chemical ChemComp-NXY / 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid


Mass: 319.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8Cl2O2S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46575 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QCB

3qcb


Resolution: 2.1→31.41 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 1983702 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 682 1.5 %RANDOM
Rwork0.233 ---
obs0.234 46385 99.3 %-
all-46385 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7919 Å2 / ksol: 0.3808 e/Å3
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 33.3288 Å2 / Biso min: 16.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2--1.31 Å20 Å2
3----5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 56 164 4781
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.281 85 1.5 %
Rwork0.269 5565 -
all-5650 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4NXY.parNXY.top

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